Zusammen

Our continuing tour free chemistry databases and Web services takes us today to BRENDA, the comprehensive enzyme information system. From the recent paper:

The BRENDA (BRaunschweig ENzyme DAtabase) (http://www.brenda-enzymes.org) represents the largest freely available information system containing a huge amount of biochemical and molecular information on all classified enzymes as well as software tools for querying the database and calculating molecular properties. The database covers information on classification and nomenclature, reaction and specificity, functional parameters, occurrence, enzyme structure and stability, mutants and enzyme engineering, preparation and isolation, the application of enzymes, and ligand-related data. The data in BRENDA are manually curated from more than 79 000 primary literature references. Each entry is clearly linked to a literature reference, the origin organism and, where available, to the protein sequence of the enzyme protein. A new search option provides the access to protein-specific data. ...

Like Biopath, BRENDA exposes of a network of reactions of small molecules mediated by enzymes. Although mainly a database of enzyme properties, BRENDA contains numerous references to small molecules and their enzymatic transformations. Unlike Biopath, most of these references are links to the primary literature.

Although Brenda doesn't appear to contain compound summary sheets, it does offer a substructure search feature. Using indole is an example molecule returned four hits including this one for 5-hydroxyindole. This BRENDA record shows 5-hydroxyindole to be involved with multiple enzymes in multiple roles including inhibitor and substrate. Selecting one of the enzymes with which 5-hydroxyindole interacts, tryptophanase, gives a summary sheet for this enzyme. Among the many pieces of information this sheet shows are the species expressing the enzyme, small molecules interacting with it, known cofactors, temperature stability, and primary literature citation.

BRENDA offers a number of other ways to search. For example, knowing the name of a pathway we can find enzymes participating in it. It's also possible to browse from a large assortment of predefined pathway types such as as apoptosis. A number of other properties can be searched, although few offer the same capability for browsing.

BRENDA is a highly interconnected database with many opportunities to follow links among its member data. However, this high level of connectivity can be somewhat confusing when trying to understand exactly what's contained in BRENDA. In addition, some items that seem like good candidates for hyperlinking are not linked; this includes the role given to structures after a substructure search (e.g., activator, inhibitor, substrate). Likewise, neither diseases nor reaction types are hyperlinked.

Enzymes play important roles both in biological and synthetic chemistry. For anyone needing information on the intersection between small molecule and enzyme chemistry, Brenda makes a good resource.

Kudos

• Data consistently linked to the primary literature.
• Documentation available from a variety of sources.
• Compilation and maintenance of data by trained specialists.

Ideas for Improvement

• First-class treatment for small molecules including dedicated molecule summary pages.
• Enable browsing for all entities (small molecules, enzymes, diseases, etc.).
• High-level overview of all small molecule transformations (analogous to Sigma-Aldrich reaction search).
• Display chemical structures in summary pages (enzyme, reaction, etc.).

Today's stop on our continuing tour of free chemistry databases and services takes us to Pherobase, a comprehensive database of peer-reviewed research relating to insects, plants, and pheromones. From the about page:

Currently, there are over 30000 entries, around 8000 molecules, and over 100000 static php pages that make it [Pherobase] the world's largest database of behaviour modifying chemicals. In addition, mass spectral, NMR, synthesis data for more than 2500 compounds are included. We are working very hard to make The Pherobase comprehensive, reliable and as complete as possible.

Pherobase was created by Ashraf M. El-Sayed from Hort Research and is supported by ISCA Technologies, developer of "environmentally friendly, natural and pheromone based tools and solutions for agricultural and urban applications," among others. Pherobase is an important example of the beneficial role the Web can play as a medium when a business need is closely aligned with the needs of a scientific community.

Pherobase offers a number of ways to explore the relationships between signaling molecules, plants, and insects. For example, we can discover the pheromones used by a particular insect genus. Or we can browse the molecules produced by various plants by functional group. Care to find out how the insect world uses hexanal? That's also possible. If we wanted to browse a list of semiochemicals useful in trapping insects, we could do that as well.

Pherobase's compound records contain chemical structures, both in 2D and 3D format, as well as links connecting molecules with the plants and animals using them. Although the site's documentation refers to mass spectral and NMR data, I was unable to find any in the records I viewed.

Pherobase also contains links to the primary literature, an extremely important feature that provides a jumping off point for those interested in further exploration.

More information on using Pherobase can be found in the online guide.

In summary, Pherobase is an excellent example of a comprehensive resource designed to serve a very specific audience, while being useful to anyone interested in the relationship between chemistry, plants, and insects.

Kudos

• Focussed, comprehensive treatment of a specific area of practical chemistry.
• Links to the primary literature.
• Many fascinating views of the data.
• Good use of both 2D and 3D chemical structures.
• Online guide.

Ideas for Improvement

• Opportunities for community involvement (e.g., "Discuss this compound" and "Edit this page") are hidden behind login dialogs with no clear instructions on how to register.
• Navigation is challenging in some cases. For example, header navigation including the links "Plants", "Insects", and "Compounds", and "Home" would be an easy fix.
• Exact- and substructure search.
• Links to Wikipedia (currently outside links point to Google keyword searches).